This vignette demonstrates how to add linkouts to a NG-CHM. Linkouts
allow for a deeper exploration of the NG-CHM data, for example by
providing direct links to NCBI Databases, GeneCards, etc.
The needed packages are loaded and a basic NG-CHM is constructed from
the sample data.
To add linkouts, the axis type is specified with
chmAddAxisType(). For the demo data in this example, row
labels correspond to genes, and are specified as HUGO gene symbols:
The column labels in the demo data are full 28-character TCGA aliquot
barcodes:
hm <- chmAddAxisType(hm, 'column', 'bio.tcga.barcode.sample.vial.portion.analyte.aliquot')
Resulting NG-CHM
Here is the resulting NG-CHM:
Available Axis Label Types
In the above example, the axis type was ‘bio.gene.hugo’. The
available axis types are:
-
bio.gene.entrezid: NCBI Entrez Gene Identifier
-
bio.gene.hugo: HUGO gene symbol
-
bio.geo.acc: GEO accession id
-
bio.go: Gene Ontology accession identifier
-
bio.mdacc.pathwayid: PathwaysWeb
pathway identifier
-
bio.mirna: miRNA identifier
-
bio.pathway.msigdb.name: msig DB pathway name
-
bio.protein.uniprotid: Uniprot protein
identifier
-
bio.pubmed: PubMed identifier
-
bio.tcga.barcode.sample: First 15 characters of
TCGA aliquot barcode
-
bio.tcga.barcode.sample.vial: First 16 characters
of TCGA aliquot barcode
-
bio.tcga.barcode.sample.vial.portion: First 19
characters of TCGA aliquot barcode
-
bio.tcga.barcode.sample.vial.portion.analyte: First
20 characters of a TCGA aliquot barcode
-
bio.tcga.barcode.sample.vial.portion.analyte.aliquot:
Full 28 character TCGA aliquot barcode
-
bio.transcript.ensembl: Ensembl transcript
identifier
-
bio.transcriptid: Entrez transcription
identifier
-
scholar: Google Scholar search term
-
search: Generic search term